Table 1 SNPs associated with mammographic DA, NDA and PD.

From: Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk

Lead SNP

Chr: position*

Gene †

Alleles ‡

MAF §

Stage

Z- Score

P -value

Stage 1+2

        

β || (s.e.)

Z -Score

P -value

P (Het)

SNPs associated with mammographic DA

 rs10034692

4:75638651

AREG

A/G

0.26

1

−4.67

3.00 × 10−6

−0.16 (0.03)

−6.35

2.12 × 10−10

0.77

     

2

−4.44

9.06 × 10−6

    

 rs12665607

6:151988322

ESR1

T/A

0.08

1

3.91

9.16 × 10−5

0.17 (0.04)

5.64

1.71 × 10−8

0.27

     

2

4.07

4.62 × 10−5

    

 rs10995190

10:63948688

ZNF365

G/A

0.16

1

−4.65

3.36 × 10−6

−0.24 (0.03)

−8.26

1.49 × 10−16

0.44

     

2

−6.96

3.51 × 10−12

    

 rs3817198

11:1865582

LSP1

T/C

0.34

1

4.17

3.06 × 10−5

0.14 (0.03)

6.47

9.67 × 10−11

0.99

     

2

4.97

6.63 × 10−7

    

 rs703556

12:101536024

IGF1

A/G

0.02

1

−5.13

2.91 × 10−7

−0.41 (0.08)

−6.27

3.74 × 10−10

0.90

     

2

−3.85

0.0001

    

 rs7289126

22:36958252

TMEM184B

C/A

0.40

1

−4.30

1.74 × 10−5

−0.11 (0.02)

−5.55

2.80 × 10−8

0.99

     

2

−3.63

0.0003

    

 rs17001868

22:39108177

SGSM3, MKL1

A/C

0.08

1

−4.42

9.99 × 10−6

−0.18 (0.03)

−7.33

2.29 × 10−13

0.74

     

2

−5.87

4.35 × 10−9

    

SNPs associated with mammographic NDA

 rs7816345

8:36965267

N/A

C/T

0.18

1

−7.37

1.77 × 10−13

−0.24 (0.03)

−9.96

2.40 × 10−23

0.09

     

2

−6.77

1.30 × 10−11

    

SNPs associated with mammographic PD

 rs186749

5:122482204

PRDM6

G/A

0.28

1

4.98

6.26 × 10−7

0.10 (0.02)

5.96

2.52 × 10−9

0.43

     

2

3.31

0.0009

    

 rs7816345

8:36965267

N/A

C/T

0.18

1

2.93

0.003

0.08 (0.02)

5.46

4.68 × 10−8

0.74

     

2

4.79

1.69 × 10−6

    

 rs7289126

22:36958252

TMEM184B

C/A

0.40

1

−4.75

1.99 × 10−6

−0.10 (0.02)

−5.86

4.68 × 10−9

0.82

     

2

−3.54

0.0004

    
  1. DA, dense area; MAF, minor allele frequency; NDA, non-dense area; PD, percent density; SNP, single-nucleotide polymorphism.
  2. *HG version 18.
  3. †Includes nearby genes.
  4. ‡Major allele (reference allele)/minor allele (effect allele).
  5. §MAF as in the 1000 Genomes project.
  6. ||β and s.e. estimates were obtained using fixed effects meta-analysis of cross-sectional studies (that is, studies that analysed density phenotypes as a quantitative trait) in unrelated individuals. Mammographic density phenotypes are square-root-transformed.
  7. P value for heterogeneity between studies.
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